I think this may be cause by the last enemy you kill to get to 100%.
The game counts everything in fractions, but rounds up to whole numbers for lists, leader boards, and other stuff.
If you need just 4% to max out a creature and the next kill would get you exactly 4%, but instead you kill it in a group and only get 3.99%. The next kill to 100% somehow give you few extra KP.
More likely however, is that the game rounds up the % points in the Knowledge Book, so when you get to 99.99% it gives you the 100% message and stops further counting, but you're not really at 100%. And therefore lose a few KP overall.
If continues to count even though it shows 100%, there is a chance you still need to kill one extra creature. (Although with my limited testing I could not prove this, and I think it stops counting when you get the 100% message.)
I'm at #3 (Naja) in the KP leader board. And I know from testing if I just collect just 41 extra KP I would get to 557 on the leader board because that particular number gets rounded up.
